How to make numpy array containing multidimensional arrays of different shape? [duplicate] - python

I am trying to generate a numpy array with elements as two other numpy arrays, as below.
W1b1 = np.zeros((256, 161))
W2b2 = np.zeros((256, 257))
Wx = np.array([W1b1, W2b2], dtype=np.object)
this gives an error:
ValueError: could not broadcast input array from shape (256,161) into shape (256).
However, if I take entirely different dimensions for of W1b1 and W2b2 then I do not get an error, as below.
A1 = np.zeros((256, 161))
A2 = np.zeros((257, 257))
A3 = np.array([A1, A2], dtype=np.object)
I do not get what is wrong in the first code and why is numpy array trying to broadcast one of the input arrays.
I have tried on below versions (Python 2.7.6, Numpy 1.13.1) and (Python 3.6.4, Numpy 1.14.1).

Don't count on np.array(..., object) making the right object array. At the moment we don't have control over how many dimensions it makes. Conceivably it could make a (2,) array, or (2, 256) (with 1d contents). Sometimes it works, sometimes raises an error. There's something of a pattern, but I haven't seen an analysis of the code that shows exactly what is happening.
For now it is safer to allocate the array, and fill it:
In [57]: arr = np.empty(2, object)
In [58]: arr[:] = [W1b1, W2b2]
np.array([np.zeros((3,2)),np.ones((3,4))], object) also raises this error. So the error arises when the first dimensions match, but the later ones don't. Now that I think about, I've seen this error before.
Earlier SO questions on the topic
numpy array 1.9.2 getting ValueError: could not broadcast input array from shape (4,2) into shape (4)
Creation of array of arrays fails, when first size of first dimension matches
Creating array of arrays in numpy with different dimensions

Related

Trace Operation in Python not Forming Correct Array Shape

I'm looking to find the trace of matrices (using Numpy) in a function I have defined in Python. The input parameters tensor and tensor_transpose are both matrices of size (N,2,2) and are extracted from a VTK file (N is a rather large number and varies depending on the file). So both A and B are arrays of (N,2,2). By taking the trace of each array (sum of the diagonal terms), a single value for each array should be returned. So np.trace(A)**3)-(np.trace(B)**3 should be a single numerical value, with the array being of shape (N,1). My output though does not show this, with the returned shape being (2,).
Can anyone explain why? Is it an issue with the trace function and is there a solution?
import numpy as np
A=np.array(0.5*(tensor-tensor_transpose))
B=np.array(0.5*(tensor+tensor_transpose))
C=np.array(0.5*((np.trace(A)**3)-(np.trace(B)**3)))
print(A.shape)
print(B.shape)
print(C.shape)
#Output
#(60600, 2, 2)
#(60600, 2, 2)
#(2,)
Maybe you need to specify the axes:
np.trace(A, axis1=1, axis2=2)

Broadcasting error when forming numpy array with elements as two other numpy arrays

I am trying to generate a numpy array with elements as two other numpy arrays, as below.
W1b1 = np.zeros((256, 161))
W2b2 = np.zeros((256, 257))
Wx = np.array([W1b1, W2b2], dtype=np.object)
this gives an error:
ValueError: could not broadcast input array from shape (256,161) into shape (256).
However, if I take entirely different dimensions for of W1b1 and W2b2 then I do not get an error, as below.
A1 = np.zeros((256, 161))
A2 = np.zeros((257, 257))
A3 = np.array([A1, A2], dtype=np.object)
I do not get what is wrong in the first code and why is numpy array trying to broadcast one of the input arrays.
I have tried on below versions (Python 2.7.6, Numpy 1.13.1) and (Python 3.6.4, Numpy 1.14.1).
Don't count on np.array(..., object) making the right object array. At the moment we don't have control over how many dimensions it makes. Conceivably it could make a (2,) array, or (2, 256) (with 1d contents). Sometimes it works, sometimes raises an error. There's something of a pattern, but I haven't seen an analysis of the code that shows exactly what is happening.
For now it is safer to allocate the array, and fill it:
In [57]: arr = np.empty(2, object)
In [58]: arr[:] = [W1b1, W2b2]
np.array([np.zeros((3,2)),np.ones((3,4))], object) also raises this error. So the error arises when the first dimensions match, but the later ones don't. Now that I think about, I've seen this error before.
Earlier SO questions on the topic
numpy array 1.9.2 getting ValueError: could not broadcast input array from shape (4,2) into shape (4)
Creation of array of arrays fails, when first size of first dimension matches
Creating array of arrays in numpy with different dimensions

how to argsort with an array of arrays

I am trying to use argsort on an array of float arrays, but faced some problem.
Here is what I try to do:
import numpy as np
z = np.array([np.array([30.9,29.0,5.87],dtype=float),np.array([20.3,1.3,8.8,4.4],dtype=float)]) # actually z is transferred from a tree using root2array whose corrseponding branches is a vector<vector<float>>
Index_list = np.argsort(z)
Then I received:
ValueError: operands could not be broadcast together with shapes (4,) (3,)
So what should I do to modify z or change the way of argsort to make it work?

Element-wise Multiplication of (x,y,1) * (x,y)

matrixADimensions = matrixA.shape # returns [901,1249,1]
matrixBDimensions = matrixB.shape # returns [901,1249]
I am trying to get the element-wise multiplication of matrixA and matrixB but I am getting the error ValueError: operands could not be broadcast together with shapes (901,1249,1) (901,1249).
I believe it has something to do with the dimensions of both matrices since they are not the same. Actually, technically they are the same since [901,1249,1] is the same thing as [901,1249] but Python does not seem to know this.
How can I multiply matrixA with matrixB?
You can use numpy.squeeze to remove single-dimensional entries from the shape of your array. So in your case, you would do:
import numpy as np
np.squeeze(matrixA) * matrixB
This has the advantage of not needing to know the position of your single-dimensional entry in your array shape (unlike taking an indexing approach such as matrixA[:,:,0]).

Convert a list of 2D numpy arrays to one 3D numpy array?

I have a list of several hundred 10x10 arrays that I want to stack together into a single Nx10x10 array. At first I tried a simple
newarray = np.array(mylist)
But that returned with "ValueError: setting an array element with a sequence."
Then I found the online documentation for dstack(), which looked perfect: "...This is a simple way to stack 2D arrays (images) into a single 3D array for processing." Which is exactly what I'm trying to do. However,
newarray = np.dstack(mylist)
tells me "ValueError: array dimensions must agree except for d_0", which is odd because all my arrays are 10x10. I thought maybe the problem was that dstack() expects a tuple instead of a list, but
newarray = np.dstack(tuple(mylist))
produced the same result.
At this point I've spent about two hours searching here and elsewhere to find out what I'm doing wrong and/or how to go about this correctly. I've even tried converting my list of arrays into a list of lists of lists and then back into a 3D array, but that didn't work either (I ended up with lists of lists of arrays, followed by the "setting array element as sequence" error again).
Any help would be appreciated.
newarray = np.dstack(mylist)
should work. For example:
import numpy as np
# Here is a list of five 10x10 arrays:
x = [np.random.random((10,10)) for _ in range(5)]
y = np.dstack(x)
print(y.shape)
# (10, 10, 5)
# To get the shape to be Nx10x10, you could use rollaxis:
y = np.rollaxis(y,-1)
print(y.shape)
# (5, 10, 10)
np.dstack returns a new array. Thus, using np.dstack requires as much additional memory as the input arrays. If you are tight on memory, an alternative to np.dstack which requires less memory is to
allocate space for the final array first, and then pour the input arrays into it one at a time.
For example, if you had 58 arrays of shape (159459, 2380), then you could use
y = np.empty((159459, 2380, 58))
for i in range(58):
# instantiate the input arrays one at a time
x = np.random.random((159459, 2380))
# copy x into y
y[..., i] = x

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